Publications

Found 1195 results
2010
Kaur A, Van PT, Busch CR, Robinson CK, Pan M, Pang WL, Reiss DJ, DiRuggiero J, Baliga NS.  2010.  Coordination of frontline defense mechanisms under severe oxidative stress. Mol Syst Biol. 6:393.
Warren SE, Armstrong A, Hamilton MK, Mao DP, Leaf IA, Miao EA, Aderem A.  2010.  Cutting edge: Cytosolic bacterial DNA activates the inflammasome via Aim2. J Immunol. 185:818-21.
Gizzatkulov NM, Goryanin II, Metelkin EA, Mogilevskaya EA, Peskov KV, Demin OV.  2010.  DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results. BMC Syst Biol. 4:109.
Lee HJ, Suk JE, Patrick C, Bae EJ, Cho JH, Rho S, Hwang D, Masliah E, Lee SJ.  2010.  Direct transfer of alpha-synuclein from neuron to astroglia causes inflammatory responses in synucleinopathies. J Biol Chem. 285:9262-72.
del Sol A, Balling R, Hood L, Galas DJ.  2010.  Diseases as network perturbations. Curr Opin Biotechnol. 21:566-71.
Jung S, Marelli M, Rachubinski RA, Goodlett DR, Aitchison JD.  2010.  Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. J Biol Chem. 285:6739-49.
Price ND, Lee S.Y.  2010.  Editorial: Systems biology for biotech applications. Biotechnology journal. 5:636-7.
Diercks AK, Schwab A, Rittgen W, Kruspel A, Heuss E, Schenkel J.  2010.  Environmental influences on the production of pre-implantation embryos. Theriogenology. 73:1238-43.
Foltz G, Yoon JG, Lee H, Ma L, Tian Q, Hood L, Madan A.  2010.  Epigenetic Regulation of Wnt Pathway Antagonists in Human Glioblastoma Multiforme. Genes & Cancer. 1:81.
Ruusuvuori P, Aijo T, Chowdhury S, Garmendia-Torres C, Selinummi J, Birbaumer M, Dudley AM, Pelkmans L, Yli-Harja O.  2010.  Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. BMC Bioinformatics. 11:248.
Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon P, Jabs EW, Nickerson DA et al..  2010.  Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 42:30-5.
Mansson M, Phipps RK, Gram L, Munro MH, Larsen TO, Nielsen KF.  2010.  Explorative solid-phase extraction (E-SPE) for accelerated microbial natural product discovery, dereplication, and purification. J Nat Prod. 73:1126-32.
Wang K, Zhang S, Weber J, Baxter D, Galas DJ.  2010.  Export of microRNAs and microRNA-protective protein by mammalian cells. Nucleic Acids Res.
Vinh DB, Ko DC, Rachubinski RA, Aitchison JD, Miller SI.  2010.  Expression of the Salmonella spp. virulence factor SifA in yeast alters Rho1 activity on peroxisomes. Mol Biol Cell. 21:3567-77.
Johanneson B, McDonnell SK, Karyadi DM, Quignon P, McIntosh L, Riska SM, Fitzgerald LM, Johnson G, Deutsch K, Williams G et al..  2010.  Family-based association analysis of 42 hereditary prostate cancer families identifies the Apolipoprotein L3 region on chromosome 22q12 as a risk locus. Hum Mol Genet. 19:3852-62.
Saleem RA, Long-O'Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemisto A, Boyle J, Rachubinski RA et al..  2010.  Genome-wide analysis of effectors of peroxisome biogenesis. PLoS OnePLoS ONE. 5
Ramsey SA, Knijnenburg TA, Kennedy KA, Zak DE, Gilchrist M, Gold ES, Johnson CD, Lampano AE, Litvak V, Navarro G et al..  2010.  Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics. 26:2071-5.
Pfenning AR, Kim TK, Spotts JM, Hemberg M, Su D, West AE.  2010.  Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways. PLoS OnePLoS ONE. 5:e10870.
Fitzgerald LM, McDonnell SK, Carlson EE, Langeberg W, McIntosh LM, Deutsch K, Ostrander EA, Schaid DJ, Stanford JL.  2010.  Genome-wide linkage analyses of hereditary prostate cancer families with colon cancer provide further evidence for a susceptibility locus on 15q11-q14. Eur J Hum Genet. 18:1141-7.
Christensen GB, Baffoe-Bonnie AB, George A, Powell I, Bailey-Wilson JE, Carpten JD, Giles GG, Hopper JL, Severi G, English DR et al..  2010.  Genome-wide linkage analysis of 1,233 prostate cancer pedigrees from the International Consortium for Prostate Cancer Genetics using novel sumLINK and sumLOD analyses. Prostate. 70:735-44.
Flamez D, Roland I, Berton A, Kutlu B, Dufrane D, Beckers MC, De Waele E, Rooman I, Bouwens L, Clark A et al..  2010.  A genomic-based approach identifies FXYD domain containing ion transport regulator 2 (FXYD2)gammaa as a pancreatic beta cell-specific biomarker. Diabetologia. 53:1372-83.
Sekedat MD, Fenyo D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT.  2010.  GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Mol Syst Biol. 6:353.
Tenenbaum D, Bare JC, Baliga NS.  2010.  GTC: A web server for integrating systems biology data with web tools and desktop applications. Source Code Biol Med. 5:7.
Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B et al..  2010.  A guided tour of the Trans-Proteomic Pipeline. Proteomics. 10:1150-9.
Auffray C, Ideker T, Galas DJ, Hood L.  2010.  The hallmarks of cancer revisited through systems biology and network modeling. Cancer Systems Biology, Bioinformatics and Medicine: Research and Clinical Applications.
Picotti P, Rinner O, Stallmach R, Dautel F, Farrah T, Domon B, Wenschuh H, Aebersold R.  2010.  High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods. 7:43-6.
Wan Y, Chiang JH, Lin CH, Arens CE, Saleem RA, Smith JJ, Aitchison JD.  2010.  Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing. Nucleic Acids Res. 38:1431-40.
Eddy JA, Hood L, Price ND, Geman D.  2010.  Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). PLoS Comput Biol. 6:e1000792.
Munson MS, Spotts JM, Niemisto A, Selinummi J, Kralj JG, Salit ML, Ozinsky A.  2010.  Image-based feedback control for real-time sorting of microspheres in a microfluidic device. Lab Chip. 10:2402-10.
Edelman L.B, Eddy JA, Price ND.  2010.  In silico models of cancer. Wiley interdisciplinary reviews. Systems biology and medicine. 2:438-59.
Miao EA, Warren SE.  2010.  Innate immune detection of bacterial virulence factors via the NLRC4 inflammasome. J Clin Immunol. 30:502-6.
Miao EA, Mao DP, Yudkovsky N, Bonneau R, Lorang CG, Warren SE, Leaf IA, Aderem A.  2010.  Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome. Proc Natl Acad Sci U S A. 107:3076-80.
Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon P, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA et al..  2010.  Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol Cell Proteomics. 9:2076-88.
Yang J, Eddy JA, Pan Y., Hategan A., Tabus I, Wang Y, Cogdell D, Price ND, Pollock RE, Lazar A.J et al..  2010.  Integrated proteomics and genomics analysis reveals a novel mesenchymal to epithelial reverting transition in leiomyosarcoma through regulation of slug. Molecular & cellular proteomics : MCP. 9:2405-13.
Yang D, Ylipaa A, Yang J, Hunt K, Pollock R, Trent J, Yli-Harja O, Shmulevich I, Nykter M, Zhang W.  2010.  An integrated study of aberrant gene copy number and gene expression in GIST and LMS. Technol Cancer Res Treat. 9:171-8.
Bare JC, Koide T, Reiss DJ, Tenenbaum D, Baliga NS.  2010.  Integration and visualization of systems biology data in context of the genome. BMC Bioinformatics. 11:382.
Amon LM, Law W, Fitzgibbon MP, Gross JA, O'Briant K, Peterson A, Drescher C, Martin DB, McIntosh M.  2010.  Integrative proteomic analysis of serum and peritoneal fluids helps identify proteins that are up-regulated in serum of women with ovarian cancer. PLoS OnePLoS ONE. 5:e11137.
Gilchrist M, Henderson, W. R. J., Morotti A, Johnson CD, Nachman A, Schmitz F, Smith KD, Aderem A.  2010.  A key role for ATF3 in regulating mast cell survival and mediator release. Blood. 115:4734-41.
Himeda CL, Ranish J, Pearson RC, Crossley M, Hauschka SD.  2010.  KLF3 regulates muscle-specific gene expression and synergizes with serum response factor on KLF binding sites. Mol Cell Biol. 30:3430-43.
Facciotti MT, Pang WL, Lo FY, Whitehead K, Koide T, Masumura K, Pan M, Kaur A, Larsen DJ, Reiss DJ et al..  2010.  Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. BMC Syst Biol. 4:64.
Youn A, Reiss DJ, Stuetzle W.  2010.  Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model. Bioinformatics. 26:1879-86.
Kim P.J, Price ND.  2010.  Macroscopic kinetic effect of cell-to-cell variation in biochemical reactions. Physical review letters. 104:148103.
Sakhanenko NA, Galas DJ.  2010.  Markov Logic Networks in the Analysis of Genetic Data. J Comput Biol.
Deutsch EW.  2010.  Mass spectrometer output file format mzML. Methods Mol Biol. 604:319-31.
Lin B, Madan A, Yoon JG, Fang X, Yan X, Kim TK, Hwang D, Hood L, Foltz G.  2010.  Massively parallel signature sequencing and bioinformatics analysis identifies up-regulation of TGFBI and SOX4 in human glioblastoma. PLoS OnePLoS ONE. 5:e10210.
Weber JA, Baxter DH, Zhang S, Huang DY, How Huang K, Jen Lee M, Galas DJ, Wang K.  2010.  The MicroRNA Spectrum in 12 Body Fluids. Clin Chem. 56:1733-41.
Handcock J, Deutsch EW, Boyle J.  2010.  mspecLINE: bridging knowledge of human disease with the proteome. BMC Med Genomics. 3:7.
Ouellet E, Lausted C, Lin T, Yang CW, Hood L, Lagally ET.  2010.  Parallel microfluidic surface plasmon resonance imaging arrays. Lab Chip. 10:581-8.
Deutsch EW.  2010.  The PeptideAtlas Project. Methods Mol Biol. 604:285-96.
Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O et al..  2010.  Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal. 3:rs4.
Erkkila T, Lehmusvaara S, Ruusuvuori P, Visakorpi T, Shmulevich I, Lahdesmaki H.  2010.  Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinformatics. 26:2571-7.
Chandrasekaran S, Price ND.  2010.  Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America. 107:17845-50.
Dilworth DJ, Saleem RA, Rogers RS, Mirzaei H, Boyle J, Aitchison JD.  2010.  QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. J Am Soc Mass Spectrom. 21:1417-22.
Eddy JA, Sung J, Geman D, Price ND.  2010.  Relative expression analysis for molecular cancer diagnosis and prognosis. Technology in cancer research & treatment. 9:149-59.
Burdick DB, Cavnor CC, Handcock J, Killcoyne S, Lin J, Marzolf B, Ramsey SA, Rovira H, Bressler R, Shmulevich I et al..  2010.  SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. BMC Bioinformatics. 11:377.
Shimada T, Park BG, Wolf AJ, Brikos C, Goodridge HS, Becker CA, Reyes CN, Miao EA, Aderem A, Gotz F et al..  2010.  Staphylococcus aureus evades lysozyme-based peptidoglycan digestion that links phagocytosis, inflammasome activation, and IL-1beta secretion. Cell Host Microbe. 7:38-49.
Arpanaei A, Winther-Jensen B, Theodosiou E, Kingshott P, Hobley TJ, Thomas OR.  2010.  Surface modification of chromatography adsorbents by low temperature low pressure plasma. J Chromatogr A. 1217:6905-16.
Sipova H, Zhang S, Dudley AM, Galas DJ, Wang K, Homola J.  2010.  Surface plasmon resonance biosensor for rapid label-free detection of microribonucleic acid at subfemtomole level. Anal Chem. 82:10110-5.
Ma S, Funk C.C, Price ND.  2010.  Systems approaches to molecular cancer diagnostics. Discovery medicine. 10:531-42.
Wang K, Lee I, Carlson G, Hood L, Galas DJ.  2010.  Systems biology and the discovery of diagnostic biomarkers. Dis Markers. 28:199-207.
Ramsey SA, Gold ES, Aderem A.  2010.  A systems biology approach to understanding atherosclerosis. EMBO Mol Med. 2:79-89.
Edelman L.B, Chandrasekaran S, Price ND.  2010.  Systems biology of embryogenesis. Reproduction, fertility, and development. 22:98-105.
Saleem RA, Aitchison JD.  2010.  Systems cell biology of the mitotic spindle. J Cell Biol. 188:7-9.
Carter GW, Rush CG, Uygun F, Sakhanenko NA, Galas DJ, Galitski T.  2010.  A systems-biology approach to modular genetic complexity. Chaos. 20:026102.
Ao P, Galas DJ, Hood L, Yin L, Zhu XM.  2010.  Towards predictive stochastic dynamical modeling of cancer genesis and progression. Interdiscip Sci. 2:140-4.
Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T et al..  2010.  Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets. Proteomics. 10:1190-5.
Schmid AK, Pan M, Sharma K, Baliga NS.  2010.  Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res.
Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D et al..  2010.  Visualization of omics data for systems biology. Nat Methods. 7:S56-68.
Mo F, Mo Q, Chen Y, Goodlett DR, Hood L, Omenn GS, Li S, Lin B.  2010.  WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. BMC Bioinformatics. 11:219.
2009
Omenn GS, Aebersold R, Paik YK.  2009.  7(th) HUPO World Congress of Proteomics: launching the second phase of the HUPOPlasma Proteome Project (PPP-2) 16-20 August 2008, Amsterdam, The Netherlands. Proteomics. 9:4-6.
Milne C.B, Kim P.J, Eddy JA, Price ND.  2009.  Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnology journal. 4:1653-70.
Boyle J, Rovira H, Cavnor C, Burdick D, Killcoyne S, Shmulevich I.  2009.  Adaptable data management for systems biology investigations. BMC Bioinformatics. 10:79.
Schiess R, Mueller LN, Schmidt A, Mueller M, Wollscheid B, Aebersold R.  2009.  Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Mol Cell Proteomics. 8:624-38.
Akiyoshi B, Nelson CR, Ranish J, Biggins S.  2009.  Analysis of Ipl1-mediated phosphorylation of the Ndc80 kinetochore protein in Saccharomyces cerevisiae. Genetics. 183:1591-5.
Peterson A, Hohmann L, Huang L, Kim B, Eng JK, Martin DB.  2009.  Analysis of RP-HPLC loading conditions for maximizing peptide identifications in shotgun proteomics. J Proteome Res. 8:4161-8.
Gstaiger M, Aebersold R.  2009.  Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet. 10:617-27.
Jeong SK, Kwon MS, Lee EY, Lee HJ, Cho SY, Kim H, Yoo JS, Omenn GS, Aebersold R, Hanash S et al..  2009.  BiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers. Proteomics. 9:3729-40.
Selinummi J, Ruusuvuori P, Podolsky I, Ozinsky A, Gold E, Yli-Harja O, Aderem A, Shmulevich I.  2009.  Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images. PLoS OnePLoS ONE. 4:e7497.
Kao SC, Wu H, Xie J, Chang CP, Ranish J, Graef IA, Crabtree GR.  2009.  Calcineurin/NFAT signaling is required for neuregulin-regulated Schwann cell differentiation. Science. 323:651-4.
Huber A, Bodenmiller B, Uotila A, Stahl M, Wanka S, Gerrits B, Aebersold R, Loewith R.  2009.  Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev. 23:1929-43.
Wang K, Zhang S, Marzolf B, Troisch P, Brightman A, Hu Z, Hood LE, Galas DJ.  2009.  Circulating microRNAs, potential biomarkers for drug-induced liver injury. Proc Natl Acad Sci U S A. 106:4402-7.
Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jorgensen C, Bader GD, Aebersold R, Pawson T, Linding R.  2009.  Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal. 2:ra39.
Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmstrom J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE et al..  2009.  Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol. 7:e48.
Theis M, Slabicki M, Junqueira M, Paszkowski-Rogacz M, Sontheimer J, Kittler R, Heninger AK, Glatter T, Kruusmaa K, Poser I et al..  2009.  Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division. EMBO J. 28:1453-65.
Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI.  2009.  Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. J Proteome Res. 8:887-99.
Sherwood CA, Eastham A, Lee LW, Risler J, Vitek O, Martin DB.  2009.  Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers. J Proteome Res. 8:4243-51.
Chung Y, Chang SH, Martinez GJ, Yang XO, Nurieva R, Kang HS, Ma L, Watowich SS, Jetten AM, Tian Q et al..  2009.  Critical regulation of early Th17 cell differentiation by interleukin-1 signaling. Immunity. 30:576-87.
Liu X, Alexiou M, Martin-Orozco N, Chung Y, Nurieva RI, Ma L, Tian Q, Kollias G, Lu S, Graf D et al..  2009.  Cutting edge: A critical role of B and T lymphocyte attenuator in peripheral T cell tolerance induction. J Immunol. 182:4516-20.
Killcoyne S, Carter GW, Smith J, Boyle J.  2009.  Cytoscape: a community-based framework for network modeling. Methods Mol Biol. 563:219-39.
Nykter M, Lahdesmaki H, Rust A, Thorsson V, Shmulevich I.  2009.  A data integration framework for prediction of transcription factor targets. Ann N Y Acad Sci. 1158:205-14.
Lin B, White JT, Wu J, Lele S, Old LJ, Hood L, Odunsi K.  2009.  Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer. Proteomics Clin Appl. 3:853-861.
Portis JL, Askovich P, Austin J, Gutierrez-Cotto Y, McAtee FJ.  2009.  The degree of folding instability of the envelope protein of a neurovirulent murine retrovirus correlates with the severity of the neurological disease. J Virol. 83:6079-86.
Stanford JL, Fitzgerald LM, McDonnell SK, Carlson EE, McIntosh LM, Deutsch K, Hood L, Ostrander EA, Schaid DJ.  2009.  Dense genome-wide SNP linkage scan in 301 hereditary prostate cancer families identifies multiple regions with suggestive evidence for linkage. Hum Mol Genet. 18:1839-48.
Kutlu B, Burdick D, Baxter D, Rasschaert J, Flamez D, Eizirik DL, Welsh N, Goodman N, Hood L.  2009.  Detailed transcriptome atlas of the pancreatic beta cell. BMC Med Genomics. 2:3.
Shmulevich I, Aitchison JD.  2009.  Deterministic and stochastic models of genetic regulatory networks. Methods Enzymol. 467:335-56.
Chan TM, Longabaugh W, Bolouri H, Chen HL, Tseng WF, Chao CH, Jang TH, Lin YI, Hung SC, Wang HD et al..  2009.  Developmental gene regulatory networks in the zebrafish embryo. Biochim Biophys Acta. 1789:279-98.
Schmidt A, Claassen M, Aebersold R.  2009.  Directed mass spectrometry: towards hypothesis-driven proteomics. Curr Opin Chem Biol. 13:510-7.
Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS.  2009.  Diurnally entrained anticipatory behavior in archaea. PLoS ONEPLoS ONE. 4:e5485.
Foltz G, Yoon JG, Lee H, Ryken TC, Sibenaller Z, Ehrich M, Hood L, Madan A.  2009.  DNA methyltransferase-mediated transcriptional silencing in malignant glioma: a combined whole-genome microarray and promoter array analysis. Oncogene. 28:2667-77.
Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE, FlyBase C, Aebersold R, Hafen E.  2009.  The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. BMC Bioinformatics. 10:59.

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